Description Details Author(s) Examples
vartools is an R-package for the analysis of rare variants and currently has the following methods: CMC, KBAC, RVE, VT, RareCover, RBT, C-alpha, etc.
Installation
git clone https://github.com/izhbannikov/vartools.git
R CMD INSTALL vartools
Package: | vartools |
Type: | Package |
Version: | 1.4.0 |
Date: | 2015-10-04 |
License: | GPL (>= 2) |
Project URL: | https://github.com/izhbannikov/vartools |
Ilya Y. Zhbannikov
Maintainer: Ilya Y. Zhbannikov | i.zhbannikov@mail.ru
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | #CMC test
# Load the package
library(vartools)
?cmc
pgdata <- as.matrix(read.table(system.file("extdata","phengen.dat",package="vartools"), as.is=T, skip = 1))
cmc.test <- cmc(table=pgdata)
print(cmc.test)
#KBAC test
?kbac
alpha <- 0.05
num.permutation <- 3000
quiet <- 1
alternative <- 1
maf.upper.bound <- 0.05
casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1)
kbac.test <- kbac(table=casectrl.dat, alpha, num.permutation, quiet, maf.upper.bound, alternative)
print(kbac.test)
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